Oxford Nanopore has announced it will be selling its rackmounted DNA …

The DNA sequencing systems on the market produce their output by synthesizing new DNA in a way that allows them to read the identity of the base that's added. There have been a few ideas floated around that involved reading the bases directly from existing molecules, but the technical challenges of doing so have kept anyone from bringing these technologies to market. Now, a company called Oxford Nanopore has announced that it will be selling a DNA-reading machine before the year is over. Not only does this represent an entirely new sequencing technology, but the systems will be sold as rack-mounted hardware that can be clustered.

The basic principle behind nanopore sequencing is pretty simple (we've got more detail if you're interested). An external voltage forces DNA molecules to snake their way through a narrow protein pore embedded in a membrane. As each base passes through, its distinct chemical properties cause changes in the voltage difference across the membrane. By tracking the local voltage changes, it's possible to identify each base as it slides through the pore.

This has some nice features; there are no enzymes or chemicals consumed as the DNA is being read, which cuts down on the cost and speeds up the reading dramatically. There's also (at least theoretically) no limit the the length of the DNA molecule that goes through the pore. If you could keep a human chromosome intact, you could potentially send the whole thing through the pore. The same system also can identify proteins and RNA, so the same hardware can be repurposed for multiple uses.

But crafting a system that matches pores to miniaturized voltage-reading hardware has turned out to be a challenge, and the speed of the system actually works to its disadvantage, making it harder to separate out the signal of each individual base.

Oxford apparently feels that it has overcome most of these problems. It's crafted a system in which a single piece of hardware can read the output of 2,000 pores simultaneously. The error rate is still substantial—according to reports, it's about four percent—but the company claims that will be reduced considerably by the time a product hits the market.

The nanopores and hardware will be sold as a removable cartridge, with each cartridge capable of processing all the samples in a standard 96-well plate. You just snap the cartridge onto a plate, and drop it into the Oxford Nanopore machines. The control software will generate sequence from a single well of the plate, until a target output is reached; it will then flush the system and move on to the next plate.

The novel thing about the hardware is that it's designed to run in parallel. Each machine is rack-mountable, and a user can set it up so that an entire rack is is working on the same sample at once (so, for example, every sample in well six could contain DNA from the same source). The whole rack would then generate sequence until the aggregate target is reached before moving on.

The ability to go massively parallel means that these machines can produce sequence at a staggering rate; Oxford is claiming that 20 of the rack units could pump out an entire human genome in 15 minutes (doing the computing to actually generate a final genome sequence would take quite a bit longer). And the costs are very competitive. Estimates are that a billion base pairs (a Gigabase) will be in the area of $30. That places a reasonable coverage of the genome at under $5,000.

Oxford clearly has the manufacturing sorted out, and it already has plans to increase the density of the nanopores on their hardware. So the question is whether it can drop the error rate and increase the length of the reads. If it can manage both of those, this technology could potentially transform genome sequencing.

In addition to the high-throughput hardware, Oxford has also announced a compact, single-use system that is actually about the size of a cell phone and plugs in to computers as a USB device. The goal for this is to provide things like rapid on-site diagnostics.

It would be pretty cool to have a scan of your DNA so you can know what to watch out for, and what not to. Obviously a lot of work would need to go into making such real-world meaning out of the markers, and such work is ongoing.

It's a little sci-fi as of now, but I think it would be great. Ignorance really isn't bliss at all.

Between this machine, the Ion Torrent, and the Illumina, the only real question seems to be whether a genome sequence will cost enough so that it can only be justified by a serious disease or a once in a lifetime expense or whether a whole genome sequence will be cheap enough that it can be done anytime someone feels like it. In either case, the implications are more or less the same and staggering. Essentially all medical practice is going to become basic research. As doctors characterize differences in the development of any disease in different patients, they will be able to correlate those differences with differences in the patients genes. Its only going to be a matter of time before people really understand what all those genes do.

And how long until I have to pay a licensing fee in order to be allowed to metabolize glucose?

This is a pretty nonsensical question. Why would you have to pay a licensing fee to metabolize glucose?

I believe he's referring to the fact that patents have been granted on naturally-occurring DNA sequences. Ars has had at least one article where, iirc, a patent was granted on the DNA sequence for breast cancer, so there's a fee paid every time a test is performed to determine if it's that type of breast cancer. Mid last year or so, I think.

So, he's implying someone will determine the sequence responsible for allowing us to metabolize glucose, patent it, then charge all organisms that possess that sequence a licensing fee for using processes derived from that DNA.

And how long until I have to pay a licensing fee in order to be allowed to metabolize glucose?

This is a pretty nonsensical question. Why would you have to pay a licensing fee to metabolize glucose?

I believe he's referring to the fact that patents have been granted on naturally-occurring DNA sequences. Ars has had at least one article where, iirc, a patent was granted on the DNA sequence for breast cancer, so there's a fee paid every time a test is performed to determine if it's that type of breast cancer. Mid last year or so, I think.

So, he's implying someone will determine the sequence responsible for allowing us to metabolize glucose, patent it, then charge all organisms that possess that sequence a licensing fee for using processes derived from that DNA.

As horrible as the patents are, the devil's advocate in me would like to point out that the licensing of tests is charging a fee for something people couldn't do before a certain point. Animals have been metabolizing glucose for billions of years. I think that's known as "prior art".

At 4% error rate just before it hits commercialization, this thing is a non-starter. Many products that are in the pre-production prototype startup stage can do over 99%. The Ion Torrent/Proton is considered to be a very mediocre sequencer and that is significantly better than what this technology can put out. Not only that, but the standard of quality is how it deals with difficult sequencing templates. In particular, long runs of single bases. Nanopore technology is notoriously bad at separating individual bases, so runs of bases is even worse. The cost issue is irrelevant when you have bad data.

I believe he's referring to the fact that patents have been granted on naturally-occurring DNA sequences. Ars has had at least one article where, iirc, a patent was granted on the DNA sequence for breast cancer, so there's a fee paid every time a test is performed to determine if it's that type of breast cancer.

A fee is paid every time a test is performed, be it for a specific oncogene allele, blood glucose or detection of a pathogen. I don't think that there are any modern diagnostic tests that are not patented. And afaik the test for the variant of the gene was the patented part.

This nanopore technology could turn out to be another disruptive development for life science research, and I'm absolutely thrilled to see this happening in my lifetime. Shit, when I started working in bioinformatics the human genome had not been sequenced yet and now we have the technology to do it in 15 minutes. Moore's law is nothing in comparison. But of course the interpretation of all this data is the bottleneck right now and will probably remain so for the foreseeable future. Even if we have very good solutions for the IT part of the equation, at the end of the day the colleagues at the bench need to do the experiments to truly understand the biology.

And how long until I have to pay a licensing fee in order to be allowed to metabolize glucose?

This is a pretty nonsensical question. Why would you have to pay a licensing fee to metabolize glucose?

I believe he's referring to the fact that patents have been granted on naturally-occurring DNA sequences. Ars has had at least one article where, iirc, a patent was granted on the DNA sequence for breast cancer, so there's a fee paid every time a test is performed to determine if it's that type of breast cancer. Mid last year or so, I think.

So, he's implying someone will determine the sequence responsible for allowing us to metabolize glucose, patent it, then charge all organisms that possess that sequence a licensing fee for using processes derived from that DNA.

Right, that's not going to happen, because in order to be granted a patent, it has to be both novel and non-obivous to a reasonably skilled practitioner of the arts (which it isn't) and someone else can't have done it earlier and published that information (which they have). The BRCA1 and BRCA2 patents were granted in 1995 (so they'll be gone in 3-4 years anyway) and post-Human Genome Project, the bar for obtaining such patents was raised significantly. Furthermore, you couldn't attempt to extract rent from everyone, you have to patent something for a specific application, not just in general. Again, the gene patents that people find dubious are specifically patents about using a particular gene to diagnose a particular condition. So, someone might have IP that claims "analyze gene X in a patient and compare it to the reference sequence listed <here> and use that to determine if that patient is at significant risk of disease Y" but if you sequenced gene X to find out about disease Q, you'd not be infringing the patent.

We were supposed to hear whether the BRCA case was going to be heard by the Supreme Court today (although they didn't actually tell us), but even if they do, I'd be very surprised if they did anything to prevent the patenting of 'isolated and purified' DNA sequences because it would disrupt the biotech sector too much (one of the Federal Circuit Judges who ruled on the case last year explicitly cited this as a reason). Given that the purpose of the patent system is "to promote the progress of science and the useful arts" and not "to let people make as much money as they can," that's rather sad, but that's life in America in 2012, unfortunately.

Part of the America Invents Act (the recent patent law reform) instructed USPTO to conduct a study on how exclusive patent licenses affect patient access to genetic diagnostic tests, and they have to submit that report to Congress in July. There is a public comment period, so if you feel strongly about it you can write to them and tell them: http://www.uspto.gov/aia_implementation/index.jsp

They had a public hearing yesterday in Alexandria, and there's another one in San Diego next month; they're webcast and archived, so you can see the arguments that the various lobbying organizations are making.

The sad thing about making USPTO conduct this report is that in 2010, the Secretary's Advisory Committee on Genetics, Health, and Society prepared a very comprehensive report on this exact topic, with lots of recommendations (full disclosure, I was involved in writing it but it was a very very very minor contribution). You can read that report here: http://oba.od.nih.gov/oba/sacghs/report ... t_2010.pdf

Between this machine, the Ion Torrent, and the Illumina, the only real question seems to be whether a genome sequence will cost enough so that it can only be justified by a serious disease or a once in a lifetime expense or whether a whole genome sequence will be cheap enough that it can be done anytime someone feels like it.

The cost of sequencing is falling faster than Moore's Law:

By the time we know enough to use genomic data in more than a handful of indications, sequencing should be cheap enough that it will be easy to do it again - at some point the slopes for sequencing cost and data storage cost might cross, although there are ways people are working on to reduce the amount of data you'd need. It might be advantageous to resequence, if you're interested in somatic or epigenetic changes, and I would think that people might be interested in looking at gene expression and RNA too.

We're working on the evidence generation now to get us there, as well as funding technology development, but it's going to take some time.

Between this machine, the Ion Torrent, and the Illumina, the only real question seems to be whether a genome sequence will cost enough so that it can only be justified by a serious disease or a once in a lifetime expense or whether a whole genome sequence will be cheap enough that it can be done anytime someone feels like it.

The cost of sequencing is falling faster than Moore's Law:

By the time we know enough to use genomic data in more than a handful of indications, sequencing should be cheap enough that it will be easy to do it again - at some point the slopes for sequencing cost and data storage cost might cross, although there are ways people are working on to reduce the amount of data you'd need. It might be advantageous to resequence, if you're interested in somatic or epigenetic changes, and I would think that people might be interested in looking at gene expression and RNA too.

We're working on the evidence generation now to get us there, as well as funding technology development, but it's going to take some time.

They're fairly intertwined. Many technologies originally developed for semi-conductor production have been applied to bio work. And of course the ever decreasing cost and increasing performance of semiconductor devices plays a huge role in our ability to do anything useful with the genome data. And in turn the demand for more computing power for bio work helps drive R&D to keep Moore's Law going.

But it's all about being able to observe and manipulate the world at its smallest discrete level. Transistors were just the early practical app to get the ball rolling. EVERYTHING follows and enables yet more.

At 4% error rate just before it hits commercialization, this thing is a non-starter. Many products that are in the pre-production prototype startup stage can do over 99%. The Ion Torrent/Proton is considered to be a very mediocre sequencer and that is significantly better than what this technology can put out. Not only that, but the standard of quality is how it deals with difficult sequencing templates. In particular, long runs of single bases. Nanopore technology is notoriously bad at separating individual bases, so runs of bases is even worse. The cost issue is irrelevant when you have bad data.

I don't think the 4% error rate will be a real issue in practice. From what I've been reading about the technology, the main error mode is deletions. I'm not sure whether the errors are specific to sequence features, but getting some depth of coverage of a sequence would make it easy to fix those errors. I've seen it mentioned that they are working on chips with different error properties, so you might be able to sequence on the different types of chips to negate errors between them.

The main benefit is the long read length. Illumina HiSeq sequencing will only give you about 150 base pairs of each end of a read. De novo assembly with these read lengths is a nightmare, compared to what you would be getting with this. I think the combination of long read length and throughput will make this technology a real winner.

Not knowing a whole lot about it, but is that a 4% repeatable error or a 4% random error? If the later and if this sucker can really run in parrellel sequencing the same genome, would you get a pretty error proof sequencing if you just sequence the same thing a few times?

Sequence it say 5 times at the same time and compare notes between the sequences. I would think that would get you from 4% error rate down to small fractions of 1%. Do it a few more times and the error rate would drop even further.

If by market they get the error rate down to say 1%, I'd think comparative analysis between a very small handful of sequences would get you effectively an error proof result.

Oxford Nanopore say it's just random, so yes, you'd expect depth of coverage would probably fix it. For clinical applications, recently I've seen suggestions that 100x-500x is necessary to get an exome or genome, although that's on current platforms, not ONT.